modified some calculators and other stuff - pds

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 62258a85661b4983ee787262f655440992087f6e..2687f9249fe3aa54b3641b0e4430e9e25da65813 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -22,7 +22,7 @@
 #include "logsd.h"
 #include "bergerparker.h"
 #include "bstick.h"
-
+#include "coverage.h"
 
 //**********************************************************************************************************************
 CollectCommand::CollectCommand(){
@@ -40,6 +40,8 @@ CollectCommand::CollectCommand(){
                                        cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
                                }else if (globaldata->Estimators[i] == "nseqs") { 
                                        cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
+                               }else if (globaldata->Estimators[i] == "coverage") { 
+                                       cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
                                }else if (globaldata->Estimators[i] == "ace") { 
                                        convert(globaldata->getAbund(), abund);
                                        cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
@@ -53,12 +55,12 @@ CollectCommand::CollectCommand(){
                                        cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
                                }else if (globaldata->Estimators[i] == "bootstrap") { 
                                        cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
-                               }else if (globaldata->Estimators[i] == "geom") { 
-                                       cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geom")));
+                               }else if (globaldata->Estimators[i] == "geometric") { 
+                                       cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
                                }else if (globaldata->Estimators[i] == "qstat") { 
                                        cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
-                               }else if (globaldata->Estimators[i] == "logsd") { 
-                                       cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logsd")));
+                               }else if (globaldata->Estimators[i] == "logseries") { 
+                                       cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
                                }else if (globaldata->Estimators[i] == "bergerparker") { 
                                        cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
                                }else if (globaldata->Estimators[i] == "bstick") {